I have 3325MB of RAM and a core 2 duo 64 bit windows system running windows 7 ultimate OS.
When I use the plugin "plugin register virtual stack slices", I observe that the registered slices are
saved one by one in my selected output directory but the saving order is not numerically sequential.
It saved files NEF1, NEF2,NEF3,NEF4 and suddenly becomes NEF10,NEF11,etc. The screen shot
of the directory , I will try to upload. It shows the sequence of saving. There were 60 files in the input directory
each of 23MB Tiff format. When the 59th file was saved, I saw a log window as below:
>>>>>>>>>>>>>>>>>>>>>>>>>>>
<Out of memory>
<All available memory (2995MB) has been>
<used. To make more available, use the>
<Edit>Options>Memory & Threads command.>
>>>>>>>>>>>>>>>>>>>>>>>>>>>
My queries :

1. Being virtual stack, I hoped that there is no memory limit and I could process 100 or 200 such files. Am I right ?
2. Why the files are not saved in the numerical order ? If so, file NEF5 would not have got distorted.
3. I feel that as the processing of about 40 files were over, memory trouble began and subsequent files were 
    wrongly processed before giving out the memory shortage error in log window.
4. I tried the virtual stack in some of the other menus but the effect is the same.
5. My requirement is to process 100 or 200 such files for use in focus stacking. Since I did not find a method to  
    combine the stack , I use the aligned images from FIJI as input in a program COMBINE ZP and the results are 
    excellent. 
6. So I processed only 45 files using virtual stack method instead of my available 70 files. There was no error.
    Using the normal method of stacking into RAM, I can process only 24 files maximum, in my system. (Linear stack 
   alignment with SIFT)

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: UPDATEABLE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: E:\Fiji64/java/win64/jdk1.6.0_24//jre
  imagej.dir => E:\Fiji64

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141015224008)
Fiji: http://fiji.sc/update/ (last check:20141023202357)

Files not up-to-date:
  4c694223 (MODIFIED) 20150217210320 jars/imagej-common-0.12.1.jar
  28763c96 (MODIFIED) 20141025210702 jars/imagej-common-0.9.0.jar
  56ab750a (MODIFIED) 20140920133924 jars/imagej-ops-0.5.0.jar
  771f88d5 (MODIFIED) 20150217210326 jars/imagej-ops-0.9.0.jar
  c8af6461 (MODIFIED) 20141025210705 jars/imagej-updater-0.6.2.jar
  a6077b46 (MODIFIED) 20150217210328 jars/imagej-updater-0.7.0.jar
  6e22d9dd (MODIFIED) 20140920133924 jars/imglib2-2.0.0-beta-26.jar
  225b3943 (MODIFIED) 20150217210314 jars/imglib2-2.2.0.jar
  fd37b4cc (LOCAL_ONLY) 20150217210331 jars/imglib2-algorithm-0.2.0.jar
  ba955d64 (MODIFIED) 20140920133924 jars/imglib2-realtransform-2.0.0-beta-26.jar
  c0b8f2de (MODIFIED) 20150217210329 jars/imglib2-realtransform-2.0.0-beta-28.jar
  5be1fcae (LOCAL_ONLY) 20150217210329 jars/imglib2-roi-0.2.0.jar
  68d72328 (MODIFIED) 20140920133928 jars/scijava-common-2.33.0.jar
  cde753a7 (MODIFIED) 20150217210317 jars/scijava-common-2.38.0.jar
  a15062e7 (LOCAL_ONLY) 20140920225015 plugins/ExtendedDepthField.txt
  a5908c2b (LOCAL_ONLY) 20140921071831 plugins/edf_3D.jar
  a66e53c8 (LOCAL_ONLY) 20140921071839 plugins/ijtools.jar